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- PDB-7rqq: Structure of chimeric antibody F10heavy_L9light with PfCSP peptid... -

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Basic information

Entry
Database: PDB / ID: 7rqq
TitleStructure of chimeric antibody F10heavy_L9light with PfCSP peptide NANPNVDP
Components
  • F10 Heavy Chain
  • L9 Kappa Chain
  • PfCSP peptide NANPNVDP
KeywordsIMMUNE SYSTEM / Malaria / Antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
Plasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsHurlburt, N.K. / Pancera, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates Foundation United States
CitationJournal: Cell Rep / Year: 2022
Title: The light chain of the L9 antibody is critical for binding circumsporozoite protein minor repeats and preventing malaria.
Authors: Wang, L.T. / Hurlburt, N.K. / Schon, A. / Flynn, B.J. / Flores-Garcia, Y. / Pereira, L.S. / Kiyuka, P.K. / Dillon, M. / Bonilla, B. / Zavala, F. / Idris, A.H. / Francica, J.R. / Pancera, M. / Seder, R.A.
History
DepositionAug 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: F10 Heavy Chain
L: L9 Kappa Chain
P: PfCSP peptide NANPNVDP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1947
Polymers48,9113
Non-polymers2824
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-33 kcal/mol
Surface area19710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.787, 84.944, 64.243
Angle α, β, γ (deg.)90.000, 103.240, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide PfCSP peptide NANPNVDP


Mass: 839.850 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Plasmodium falciparum 3D7 (eukaryote)

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Antibody , 2 types, 2 molecules HL

#1: Antibody F10 Heavy Chain


Mass: 24474.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293E / Production host: Homo sapiens (human)
#2: Antibody L9 Kappa Chain


Mass: 23597.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293E / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 222 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5 / Details: 0.1M Na Citrate, pH 3.5, 1.5M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.009 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 1.89→42.47 Å / Num. obs: 62927 / % possible obs: 93.8 % / Redundancy: 3.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.028 / Rrim(I) all: 0.052 / Net I/σ(I): 12.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.89-1.932.40.311358515020.8720.2360.3932.465.8
9.06-42.473.20.02410393290.9990.0160.02926.794.8

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7RQP

7rqp


Resolution: 1.89→42.47 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.204 3704 5.98 %
Rwork0.1612 58218 -
obs0.1638 61922 87.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.85 Å2 / Biso mean: 42.1801 Å2 / Biso min: 18.93 Å2
Refinement stepCycle: final / Resolution: 1.89→42.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3349 0 17 218 3584
Biso mean--57.28 46.07 -
Num. residues----437
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.89-1.910.3031830.27371411149456
1.91-1.940.3119960.23071535163159
1.94-1.970.20571040.20821665176966
1.97-20.25051180.20481802192072
2-2.030.22571220.20641972209477
2.03-2.060.27441480.19662224237287
2.06-2.10.2371410.18432348248993
2.1-2.140.22781620.17252508267096
2.14-2.180.18621530.16782420257397
2.18-2.220.22251540.17462479263396
2.22-2.270.20211580.17712436259495
2.27-2.320.27081540.17022428258296
2.32-2.380.211620.16742461262395
2.38-2.450.21951520.16412377252994
2.45-2.520.23271530.15982451260495
2.52-2.60.19861550.16642413256896
2.6-2.690.23671580.16872461261996
2.69-2.80.23181530.1792410256394
2.8-2.930.21721460.16522334248092
2.93-3.080.23781500.17112324247491
3.08-3.270.20831530.16372322247591
3.27-3.530.21321440.15282297244190
3.53-3.880.16961460.14232249239588
3.88-4.440.17271480.12782229237788
4.44-5.590.14821420.13412337247991
5.6-42.470.21381490.18242325247491
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.84390.0804-0.37740.64760.22410.40480.05580.4761-0.1242-0.18910.00040.0217-0.1233-0.1759-0.03390.071-0.05430.0340.10420.06450.112535.953-6.37616.901
21.4760.20660.67911.07260.04151.5225-0.04320.17950.1459-0.0967-0.01390.2059-0.1256-0.23750.05770.23780.04910.03590.26930.00170.244633.18911.88917.329
39.19790.6305-5.65912.0385-0.84943.5904-0.0142-1.00310.110.5022-0.0517-0.66670.02210.85770.06150.27560.0003-0.04860.35650.02520.31159.285-4.44936.024
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND ( RESID 1:222 OR RESID 301:301 ) )H1 - 222
2X-RAY DIFFRACTION1( CHAIN H AND ( RESID 1:222 OR RESID 301:301 ) )H301
3X-RAY DIFFRACTION2( CHAIN L AND RESID 1:212 )L1 - 212
4X-RAY DIFFRACTION3( CHAIN P AND RESID 106:111 )P106 - 111

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